Templates (and css etc.) are an integral feature of decently functional wikis, but are necessarily (because of MediaWiki) an afterthought: "Just export the ones you need from Wikipedia".

Most wikis make very little if any use of templates because the maker/admin wants a wiki they can get on with adding content. Templates are difficult and a lot of extra work to get right. Having to learn how to write and debug templates, Lua, etc. or to fix the imports from Wikipedia to work okay enough, removing Wikipedia-centric cruft, e.g. the confusion of templates transcluding other templates.

Duplication of effort as every wiki admin has to start afresh with creating/importing the templates that wiki needs.